[gmx-users] Diffusion coefficient water

[li he]

4. you could even try NVT ensemble

2016-08-18 2:25 GMT+08:00 li he <parachuternewyork at gmail.com>:

> I think you could try following things to see if you could get 'better'
> results
> 1. use time step of 0.2 or even 0.1 fs
> 2. try different tau-t and tau-p, e.g. use larger tau-t
> 3. try different p-coupling methods
>
> 2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda <
> amanda.diez10 at imperial.ac.uk>:
>
>> Dear Gromacs users,
>>
>> I was trying to reproduce the published values for the diffusion
>> coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s  )before using it in
>> some of my simulations and I am failing to do so.
>> More worryingly I get different results for different identical runs.
>> I am using a 2nm side cubic cell containing 221 water molecules and a
>> time step of 0.5fs (larger timestep results in a warning since I am not
>> applying any constraints).
>> I ran 6 identical simulations (only difference is the random initial
>> velocities) and I got these different values and error magnitudes.
>> The trajectories are 10ns long. I discarded the first 2ns for the msd
>> calculation.
>>
>>  Nth Simulation         Diffusion Coefficient (x 10^-9 m^2/s)
>>
>>             1                              2.95  +/-  0.071
>>             2                              2.71  +/-  0.158
>>             3                              2.52  +/-   0.007
>>             4                              2.96   +/-   0.26
>>             5                              2.62   +/-  0.07
>>             6                              2.71  +/-  0.158
>>
>> Is it normal that I get different results like this?  (Despite averaging
>> over more than 7ns and 221 molecules?).
>>
>> Many thanks in advance.  Below are the detailed parameters.
>>
>> Amanda
>>
>> Detailed parameters:
>>
>> nstlist                 = 10
>>
>> ns_type                 = grid
>>
>> rlist                   = 0.9
>>
>> coulombtype             = PME
>>
>> rcoulomb                = 0.9
>>
>> fourierspacing          = 0.12
>>
>> pme_order               = 4
>>
>> ewald_rtol              = 1e-6
>>
>> vdw-type                = cut-off
>>
>> rvdw                    = 0.9
>>
>> pbc                     = xyz
>>
>> tcoupl                  = nose-hoover
>>
>> tc_grps                 = SYSTEM
>>
>> tau_t                   = 0.4
>>
>> ref_t                   = 298
>>
>> nsttcouple              =-1
>>
>> nh-chain-length         = 1
>>
>> pcoupl                  = Berendsen
>>
>> pcoupltype              = isotropic
>>
>> tau_p                   = 10.0
>>
>> compressibility         = 4.5e-5
>>
>> ref_p                   = 1.01325
>>
>> refcoord-scaling        = all
>>
>> DispCorr                = EnerPres
>>
>> gen_vel                 = yes
>>
>> gen_temp                = 293
>>
>> gen_seed                = -1
>>
>> constraints             = none
>> --
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>
>